7DOB | pdb_00007dob

Crystal structure of Catabolite repressor activator (Apo)

• PDB DOI: https://doi.org/10.2210/pdb7DOB/pdb

• Classification: GENE REGULATION
• Organism(s): Escherichia coli 536
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-13 Released: 2021-12-22 
• Deposition Author(s): Neetu, N., Katiki, M., Kumar, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.273 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.227 (Depositor) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Catabolite repressor activator (Apo)

Neetu, N., Katiki, M., Kumar, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 41.05 kDa 
• Atom Count: 2,320 
• Modeled Residue Count: 277 
• Deposited Residue Count: 357 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catabolite repressor/activator	A	357	Escherichia coli 536	Mutation(s): 0  Gene Names: ECP_0082
UniProt
Find proteins for A0A454A0X5 (Escherichia coli O6:K15:H31 (strain 536 / UPEC)) Explore A0A454A0X5  Go to UniProtKB:  A0A454A0X5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO (Subject of Investigation/LOI)	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.273 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.227 (Depositor) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.577	α = 90
b = 102.577	β = 90
c = 160.328	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Neetu, N., Katiki, M., Kumar, P.

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description